Merge pull request #155 from cmu-delphi/djm/endpointfun

Djm/endpointfun

Author: dshemetov

.Rbuildignore

@@ -3,11 +3,10 @@
 ^.*\.Rproj$
 ^.*\..Rcheck$
 ^\.Rproj\.user$
-
+^DEVELOPMENT\.md$
 ^doc$
 ^shiny$
 ^docs$
-^Meta$
 ^_pkgdown\.yml$
 ^pkgdown$
 ^data-raw$

.github/workflows/ci.yml

@@ -7,23 +7,21 @@ on:
 jobs:
   build:
     runs-on: ubuntu-20.04
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
     steps:
       - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          r-version: 4.0
-
-      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::devtools, any::rcmdcheck, local::.
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         env:
           DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}
-        with:
-          args: 'c("--no-manual", "--as-cran")'
-          error-on: '"error"'

vignettes/development.rmd renamed to DEVELOPMENT.md

@@ -1,19 +1,3 @@
----
-title: "Notes for Developers"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{Notes for Developers}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-```{r setup, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-```
-
 ## Development Environment
 
 Relevant R commands

Meta/vignette.rds

@@ -6,6 +6,7 @@ S3method(print,covidcast_data_signal)
 S3method(print,covidcast_data_source)
 S3method(print,epidata_call)
 export("%>%")
+export(avail_endpoints)
 export(covid_hosp_facility)
 export(covid_hosp_facility_lookup)
 export(covid_hosp_state_timeseries)

NAMESPACE

@@ -0,0 +1,20 @@
+#' List all available endpoints
+#'
+#' @return A [`tibble::tibble`] with 2 columns. `Endpoint` contains the function
+#'   for accessing the Delphi Epidata API endpoint along with a `Description`.
+#' @export
+#'
+#' @examples
+#' endps <- avail_endpoints()
+#' print(endps, n = nrow(endps))
+avail_endpoints <- function() {
+  h <- help.search("endpoint",
+    package = "epidatr", fields = "concept",
+    agrep = FALSE
+  )$matches
+  tib <- tibble::tibble( # printing is much nicer than data.frame
+    Endpoint = paste0(h$Name, "()"),
+    Description = h$Title
+  )
+  tib
+}

R/avail_endpoints.R

@@ -61,32 +61,34 @@ parse_source <- function(source, base_url) {
 
 #' @method as.data.frame covidcast_data_signal_list
 #' @export
-as.data.frame.covidcast_data_signal_list <- function(signals, ...) {
-  as.data.frame(do.call(rbind, lapply(signals, function(x) {
-    sub <- x[c(
-      "source",
-      "signal",
-      "name",
-      "active",
-      "short_description",
-      "description",
-      "time_type",
-      "time_label",
-      "value_label",
-      "format",
-      "category",
-      "high_values_are",
-      "is_smoothed",
-      "is_weighted",
-      "is_cumulative",
-      "has_stderr",
-      "has_sample_size"
-    )]
-    sub$geo_types <- paste0(names(x$geo_types), collapse = ",")
-    sub
-  })), row.names = sapply(signals, function(x) {
-    x$key
-  }), ...)
+as.data.frame.covidcast_data_signal_list <- function(x, ...) {
+  as.data.frame(
+    do.call(rbind, lapply(x, function(z) {
+      sub <- z[c(
+        "source",
+        "signal",
+        "name",
+        "active",
+        "short_description",
+        "description",
+        "time_type",
+        "time_label",
+        "value_label",
+        "format",
+        "category",
+        "high_values_are",
+        "is_smoothed",
+        "is_weighted",
+        "is_cumulative",
+        "has_stderr",
+        "has_sample_size"
+      )]
+      sub$geo_types <- paste0(names(z$geo_types), collapse = ",")
+      sub
+    })),
+    row.names = sapply(x, function(y) y$key),
+    ...
+  )
 }
 
 #' @export
@@ -152,18 +154,29 @@ covidcast_epidata <- function(base_url = global_base_url, timeout_seconds = 30)
 
 #' @method as.data.frame covidcast_data_source_list
 #' @export
-as.data.frame.covidcast_data_source_list <- function(sources, ...) {
-  as.data.frame(do.call(rbind, lapply(sources, function(x) {
-    sub <- x[c(
-      "source", "name", "description", "reference_signal", "license"
-    )]
-    sub$signals <- paste0(sapply(x$signals, function(y) {
-      y$signal
-    }), collapse = ",")
-    sub
-  })), row.names = sapply(sources, function(x) {
-    x$source
-  }), ...)
+as.data.frame.covidcast_data_source_list <- function(x, ...) {
+  as.data.frame(
+    do.call(
+      rbind,
+      lapply(
+        x,
+        FUN = function(z) {
+          cols <- c(
+            "source", "name", "description", "reference_signal",
+            "license"
+          )
+          sub <- z[cols]
+          sub$signals <- paste0(
+            sapply(z$signals, function(y) y$signal),
+            collapse = ","
+          )
+          sub
+        }
+      )
+    ),
+    row.names = sapply(x, function(z) z$source),
+    ...
+  )
 }
 
 print.covidcast_epidata <- function(x, ...) {